% For all reversible reactions, the following equation holds true for the
% reverse direction: vi + c * vrxnC >= u.

I think this should be vi + c * vrxnC >= -u

% The output is a coupled model (modelCoupled), in which for every new
% entry in modelCoupled.b a "slack" variable has been added
% to modelCoupled.mets.

If one runs

model=createModel();
model=addReaction(

https://github.com/SBRG/ssbio/blob/6f41652f716681a64f2f57aa3cc47eb1953e4ae4/docs/tutorials.ipynb#L7

There are two issues I've found running this code:

1. I think shutil.which is only availible for python3 but the ipython notbook defaults to opening in python2. I switched to using subprocess and it works fine

def check_path(path):
    """Check if the specified program is in the PA

Description of the issue:

• It would be great if delta G field can be added for each reaction/metabolite
• Metacyc offers this information at pH 7.3 and ionic strength 0.25.

I hereby confirm that I have:

• Followed the guidelines to install RAVEN.
• Checked that a similar issue does not [already exist](https

It seems as if the Latest commit
9bc1b6b
on 2 Apr was incompletely merged, or something to that effect...

contribute('opencobra/COBRA.tutorials')

   ~~~ COBRA.tutorials ~~~


  (You can abort any process using CTRL+C)

  [1] Start a new branch.
  [2] Select an existing branch to work on.
  [3] Publish a branch.
  [4] Delete a branch.
  [5] Update t

First I'll just mention that this library is awesome! Thank you for all your hard work on it. We're currently using it to simulate patient physiology in a branch of our synthetic patient generator which will hopefully get pulled into a release in the near future.

So, to the issue at hand:

It would be helpful to know which version

Any thoughts on what gene catalyzes reaction R_y000208?

It is present in most yeasts but notably absent in the Yarli reference genome. I tried searching with BLASTP/BLASTN but had no luck.

https://www.genome.jp/dbget-bin/get_linkdb?-t+genes+rn:R01954

edit by @edkerk:

• confirm that reactions from SI Table 1 are present in the model
• change rxnNotes for these reactions, to men